bulk - Calculates the average bulkiness of amino acid sequences
bulk calculates the average bulkiness score of amino acid sequences.
Non-informative positions are excluded, where non-informative is defined as any
c("X", "-", ".", "*").
bulk(seq, bulkiness = NULL)
- vector of strings containing amino acid sequences.
- named numerical vector defining bulkiness scores for
each amino acid, where names are single-letter amino acid
character codes. If
NULL, then the Zimmerman et al, 1968 scale is used.
A vector of bulkiness scores for the sequence(s).
- Zimmerman JM, Eliezer N, Simha R. The characterization of amino acid sequences in proteins by statistical methods. J Theor Biol 21, 170-201 (1968).
# Default bulkiness scale seq <- c("CARDRSTPWRRGIASTTVRTSW", "XXTQMYVRT") bulk(seq)
 14.46227 16.58857
# Use the Grantham, 1974 side chain volumn scores from the seqinr package library(seqinr) data(aaindex) x <- aaindex[["GRAR740103"]]$I # Rename the score vector to use single-letter codes names(x) <- translateStrings(names(x), ABBREV_AA) # Calculate average volume bulk(seq, bulkiness=x)
 77.34091 93.71429
For additional size related indices see aaindex.